rs6076080

chr20-23511141-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000619495.1(ENSG00000260202):n.438+7476G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,252 control chromosomes in the GnomAD database, including 682 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.082 (682 hom., cov: 33)
• Consequence: ENST00000619495.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000619495.1	n.438+7476G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0817 AC: 12432 AN: 152134 Hom.: 680 Cov.: 33

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0765

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0817 AC: 12438 AN: 152252 Hom.: 682 Cov.: 33 AF XY: 0.0818 AC XY: 6089 AN XY: 74446

Gnomad4 AFR AF: 0.0242

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0700

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.0704

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0987 Hom.: 460

Bravo AF: 0.0835

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.3
Dann	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6076080; hg19: chr20-23491778;